Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points. More...
#include <IdealizeMover.hh>
Public Types | |
| typedef core::Real | Real |
| typedef core::pose::Pose | Pose |
 Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
Public Member Functions | |
| IdealizeMover () | |
| moves::MoverOP | clone () const override |
| clone has to be overridden only if clone invocation is expected. More... | |
| moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| IdealizeMover & | atom_pair_constraint_weight (core::Real const setting) |
| IdealizeMover & | coordinate_constraint_weight (core::Real const setting) |
| IdealizeMover & | fast (bool const setting) |
| IdealizeMover & | chainbreaks (bool const setting) |
| IdealizeMover & | cis_omega (bool const setting) |
| IdealizeMover & | report_CA_rmsd (bool const setting) |
| void | apply (Pose &pose) override |
| Main Method. More... | |
| void | set_pos_list (utility::vector1< core::Size > pos_list) |
| Sets the list of residue positions to idealize. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| core::select::residue_selector::ResidueSelectorCOP | ignore_residues_in_csts () const |
| void | ignore_residues_in_csts (core::select::residue_selector::ResidueSelectorCOP const &i) |
| void | impose_constraints (bool const i) |
| bool | impose_constraints () const |
| bool | constraints_only () const |
| void | constraints_only (bool const c) |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
Private Member Functions | |
| void | setup_idealize_constraints (Pose &pose) |
| Add the idealize constraints to the pose's constraint set. More... | |
Private Attributes | |
| utility::vector1< core::Size > | pos_list_ |
| Real | atom_pair_constraint_weight_ |
| Real | coordinate_constraint_weight_ |
| core::select::residue_selector::ResidueSelectorCOP | ignore_residues_in_csts_ |
| bool | cis_omega_ |
| bool | fast_ |
| bool | chainbreaks_ |
| bool | report_CA_rmsd_ |
| bool | impose_constraints_ |
| bool | constraints_only_ |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Detailed Description
Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points.
Member Typedef Documentation
◆ Pose
◆ Real
Constructor & Destructor Documentation
◆ IdealizeMover()
|
inline |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::all_atom_rmsd(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, protocols::idealize::basic_idealize(), core::scoring::CA_rmsd(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dst, core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), core::scoring::pro_close, core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::idealize::TR(), and core::pose::virtual_type_for_pose().
Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::rna::denovo::create_rna_vall_torsions(), protocols::denovo_design::components::extract_sheets_from_pose(), protocols::abinitio::AbrelaxApplication::fold(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), protocols::struct_fragment::StructFragmentMover::steal_fragments(), and protocols::jobdist::universal_main().
◆ atom_pair_constraint_weight()
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inline |
References atom_pair_constraint_weight_.
◆ chainbreaks()
|
inline |
References chainbreaks_.
Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply().
◆ cis_omega()
|
inline |
References cis_omega_.
◆ clone()
|
inlineoverridevirtual |
clone has to be overridden only if clone invocation is expected.
Reimplemented from protocols::moves::Mover.
◆ constraints_only() [1/2]
|
inline |
References constraints_only_.
◆ constraints_only() [2/2]
|
inline |
References constraints_only_.
◆ coordinate_constraint_weight()
|
inline |
References coordinate_constraint_weight_.
◆ fast()
|
inline |
References fast_.
Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::rna::denovo::create_rna_vall_torsions(), protocols::abinitio::AbrelaxApplication::fold(), protocols::antibody::GraftOneCDRLoop::init(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), protocols::struct_fragment::StructFragmentMover::steal_fragments(), and protocols::jobdist::universal_main().
◆ fresh_instance()
|
inlineoverridevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ ignore_residues_in_csts() [1/2]
| core::select::residue_selector::ResidueSelectorCOP protocols::idealize::IdealizeMover::ignore_residues_in_csts | ( | ) | const |
◆ ignore_residues_in_csts() [2/2]
| void protocols::idealize::IdealizeMover::ignore_residues_in_csts | ( | core::select::residue_selector::ResidueSelectorCOP const & | i | ) |
◆ impose_constraints() [1/2]
|
inline |
References impose_constraints_.
◆ impose_constraints() [2/2]
|
inline |
References impose_constraints_.
◆ mover_name()
|
static |
Referenced by protocols::idealize::IdealizeMoverCreator::keyname().
◆ parse_my_tag()
|
overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References core::pose::get_resnum_selector(), and protocols::idealize::TR().
◆ provide_xml_schema()
|
static |
◆ report_CA_rmsd()
|
inline |
References report_CA_rmsd_.
Referenced by protocols::match::downstream::LigandConformerBuilder::initialize_conformers().
◆ set_pos_list()
|
inline |
Sets the list of residue positions to idealize.
References pos_list_.
◆ setup_idealize_constraints()
|
private |
Add the idealize constraints to the pose's constraint set.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::conformation::Residue::atom_type(), core::pose::Pose::conformation(), core::select::get_residues_from_subset(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_heavyatom(), core::chemical::AtomType::is_polar_hydrogen(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::idealize::TR(), and core::conformation::Residue::xyz().
Member Data Documentation
◆ atom_pair_constraint_weight_
|
private |
Referenced by atom_pair_constraint_weight().
◆ chainbreaks_
|
private |
Referenced by chainbreaks().
◆ cis_omega_
|
private |
Referenced by cis_omega().
◆ constraints_only_
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private |
Referenced by constraints_only().
◆ coordinate_constraint_weight_
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private |
Referenced by coordinate_constraint_weight().
◆ fast_
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private |
Referenced by fast().
◆ ignore_residues_in_csts_
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private |
◆ impose_constraints_
|
private |
Referenced by impose_constraints().
◆ pos_list_
|
private |
Referenced by set_pos_list().
◆ report_CA_rmsd_
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private |
Referenced by report_CA_rmsd().
The documentation for this class was generated from the following files:
- src/protocols/idealize/IdealizeMover.hh
- src/protocols/idealize/IdealizeMover.cc
